Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-chemoinformatics-molecular-iogit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-molecular-io)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-molecular-io"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-molecular-io/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-molecular-io"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-molecular-io.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00101 | $0.03970 |
| Opus 5 | $0.00051 | $0.01985 |
| Sonnet 5 | $0.00020 | $0.00794 |
| Haiku 4.5 | $0.00010 | $0.00397 |
Grade A, and why
bio-molecular-io scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.run(['obabel', 'docked.pdbqt', '-O', 'docked.sdf'], check=True) This is a copy
92% identical to bio-molecular-io — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 278 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: RDKit 2024.09+, Open Babel 3.1.1+, ChEMBL structure_pipeline 1.2+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
obabel -V;obabel -L formats
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Molecular I/O
Parse, write, and convert molecular file formats. Most downstream errors trace back to silent I/O issues: incorrect aromaticity perception, lost stereochemistry, mishandled charges, dropped stereo bonds, or non-canonical tautomers. This skill enumerates each format's failure modes and prescribes the correct toolchain for each scenario.
For full standardization (canonicalization, salt stripping, tautomer enumeration) see chemoinformatics/molecular-standardization. For generating 3D conformers from parsed 2D molecules, see chemoinformatics/conformer-generation.
Format Taxonomy
| Format | Dim | Stereo | Charges | Strength | Fails when |
|---|---|---|---|---|---|
| SMILES | 2D | Atom chirality @/@@; double-bond / and \ |
Atom-local formal charges | Compact, web-friendly, fast parse | Loses absolute coordinates; aromatic perception ambiguous across toolkits; tautomers not canonical |
| InChI | 2D | /b, /t, /m, /s stereo sublayers |
/q charge and /p added/removed-proton sublayers; /p is not a pH model |
Canonical by construction; cross-toolkit identity | Standard InChI normalizes mobile-H forms; limited organometallic stereo; large molecules may require special handling |
| SDF V2000 | 2D/3D | Wedge bonds | M CHG line | Industry default; metadata via tags | 999-atom limit; cannot encode multi-component reactions; query atoms ambiguous |
| SDF V3000 | 2D/3D | Wedge + stereo flag | Inline charge | No atom limit; query support; rich properties | Some software (legacy) cannot read; verbose |
| MOL2 (Tripos) | 3D | Common records rely on 3D coordinates and toolkit perception; no portable explicit stereo field | Per-atom partial | SYBYL atom types preserved for docking | Atom-type dialects diverge (SYBYL vs Corina); RDKit MOL2 parser brittle |
| PDB | 3D | None | None standard | Universal protein format | No bond orders; aromatic perception lost; ligand names truncated to 3 chars |
| PDBQT | 3D | None | Gasteiger / AD4 | AutoDock-ready; torsion tree encoded | Specific to docking; no aromaticity layer |
| BinaryCIF (MMTF retired) | 3D | Encoded | Encoded | BinaryCIF (.bcif) is the current compact structural format; RCSB stopped serving MMTF files on July 2, 2024 and recommends BinaryCIF (RCSB PDB 2024) |
Not all toolkits parse; binary format |
| CDX/CDXML | 2D | Drawing | Drawing | ChemDraw native | Not a structural format; converts unreliably |
| InChIKey | Hash | Stereo layer | n/a | Database key, fast lookup | Collision probability depends on key block and collection size; cannot recover structure |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 278 lines · 101 tokens per session scan A 819be9fa3a61
bio-molecular-io is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 101 tokens to every session and 3,970 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). It is 92% identical to bio-molecular-io, differing in 12 lines, and is treated as a copy.
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